Merge branch 'dev' into quarto

Author: delfiterradas

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+-[[#510]](https://github.com/nf-core/differentialabundance/pull/510) - Add decoupler module to differential functional enrichment subworkflow. ([@antoniasaracco](https://github.com/antoniasaracco), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@grst](https://github.com/grst)).
+
 - [[#473](https://github.com/nf-core/differentialabundance/pull/473)] - Allow formula-based contrasts in DESEQ2. ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@grst](https://github.com/grst)).
 - [[#443](https://github.com/nf-core/differentialabundance/pull/443)] - Add toolsheet-related implementations. ([@suzannejin](https://github.com/suzannejin), review by [@pinin4fjords](https://github.com/pinin4fjords), [@mirpedrol](https://github.com/mirpedrol) and [@JoseEspinosa](https://github.com/JoseEspinosa))
 - [[#450](https://github.com/nf-core/differentialabundance/pull/441)] - Allow usage of strings for makeContrasts in DREAM. ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords), [@suzannejin](https://github.com/suzannejin) and [@grst](https://github.com/grst)).
@@ -25,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [[#476](https://github.com/nf-core/differentialabundance/pull/476)] - Fixed null.csv and warning at top of report ([@SusiJo](https://github.com/SusiJo), reviewed by [@pinin4fjords](https://github.com/pinin4fjords), [@atrigila](https://github.com/atrigila), [@maxulysse](https://github.com/maxulysse))
 - [[#358](https://github.com/nf-core/differentialabundance/pull/358)] - Fixed nf-tests not running due to `--changed-since HEAD^`([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#344](https://github.com/nf-core/differentialabundance/pull/344)] - Fixed replacement of NA sub-strings
   ([@atrigila](https://github.com/atrigila), suggested by [@BEFH](https://github.com/BEFH), review by [@apeltzer](https://github.com/apeltzer) and [@nschcolnicov](https://github.com/nschcolnicov))
@@ -40,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [[#476](https://github.com/nf-core/differentialabundance/pull/476)] - Update documentation & report fixes ([@SusiJo](https://github.com/SusiJo), reviewed by [@pinin4fjords](https://github.com/pinin4fjords), [@atrigila](https://github.com/atrigila), [@maxulysse](https://github.com/maxulysse))
 - [[#468](https://github.com/nf-core/differentialabundance/pull/468)] - Template update for nf-core/tools v3.3.1 ([@SusiJo](https://github.com/SusiJo), reviewed by [@famosab](https://github.com/famosab), [@mashehu](https://github.com/mashehu))
 - [[#448](https://github.com/nf-core/differentialabundance/pull/448)] - Simplify toolsheet handling and restructure workflow to use paramset in meta. ([@pinin4fjords](https://github.com/pinin4fjords), review by [@suzannejin](https://github.com/suzannejin) and [@grst](https://github.com/grst))
 - [[#431](https://github.com/nf-core/differentialabundance/pull/431)] - Replace the calls to differential and functional analysis modules by subworkflows. ([@suzannejin](https://github.com/suzannejin), review by [@pinin4fjords](https://github.com/pinin4fjords))

assets/differentialabundance_report.qmd

@@ -1023,8 +1023,8 @@ if (!is.null(params$meta$params$functional_method)){
             cat("\n##### ", gmt_name ,"\n")
             cat("::: {.panel-tabset}", "\n")
 
-            reference_gsea_tables <- paste0(differential_names, ".", gmt_name, '.gsea_report_for_', gsea_contrasts$reference, '.tsv')
-            target_gsea_tables <- paste0(differential_names, ".", gmt_name, '.gsea_report_for_', gsea_contrasts$target, '.tsv')
+            reference_gsea_tables <- paste0(gsea_contrasts$id, ".", gmt_name, '.gsea_report_for_', gsea_contrasts$reference, '.tsv')
+            target_gsea_tables <- paste0(gsea_contrasts$id, ".", gmt_name, '.gsea_report_for_', gsea_contrasts$target, '.tsv')
 
             for (i in seq_len(nrow(gsea_contrasts))) {
                 cat("\n###### ", contrast_descriptions[i], "\n")
@@ -1062,10 +1062,11 @@ if (!is.null(params$meta$params$functional_method)){
         ifelse(params$meta$params$gprofiler2_significant, paste0(" Enrichment was only considered if significant, i.e. adjusted p-value <= ", params$meta$params$gprofiler2_max_qval, "."), "Enrichment was also considered if not significant."), "\n"))
 
         # Make sure to grab only non-empty files
-        for (name in differential_names) {
+        for (i in seq_along(differential_names)) {
+            name <- differential_names[i]
             cat(paste0("\n##### ", name, "\n"))
 
-            table <- paste0(name, ".gprofiler2.all_enriched_pathways.tsv")
+            table <- paste0(contrasts$id[i], ".gprofiler2.all_enriched_pathways.tsv")
             table_path <- file.path(params$input_dir, table)
             if (!file.exists(table_path) || file.size(table_path) == 0){
                 cat(paste0("No ", ifelse(params$meta$params$gprofiler2_significant, "significantly", ""), " enriched pathways were found for this contrast."))

conf/modules.config

@@ -375,6 +375,7 @@ process {
 
     withName: GSEA_GSEA {
         ext.prefix = { "${meta.id}.${gene_sets.baseName}." }
+
         publishDir = [
             [
                 path: { "${params.outdir}/report/gsea/${meta.id}/${gene_sets.baseName}" },
@@ -463,6 +464,34 @@ process {
         ].join(' ').trim() }
     }
 
+    withName: DECOUPLER_DECOUPLER {
+        ext.prefix = {
+            def method = meta.params.differential_method ?: meta.differential_method ?: "unknown"
+            def prefix = "${method}_${meta.id}"
+            return prefix
+        }
+        ext.args = {
+            def features_id = meta.params?.features_id_col ?: 'gene_id'
+            def features_symbol = meta.params?.features_name_col ?: 'gene_name'
+            def min_n = meta.params?.decoupler_min_n ?: 5
+            def methods = meta.params?.decoupler_methods ?: 'mlm'
+
+            "--min_n ${min_n} --transpose TRUE --ensembl_ids TRUE --methods ${methods} --features_id_col ${features_id} --features_symbol_col ${features_symbol} --column ${params.differential_fc_column}"
+        }
+        publishDir = [
+            [
+                path: { "${params.outdir}/tables/decoupler" },
+                mode: params.publish_dir_mode,
+                pattern: '*.tsv'
+            ],
+            [
+                path: { "${params.outdir}/plots/decoupler" },
+                mode: params.publish_dir_mode,
+                pattern: '*_estimate_decoupler_plot.png'
+            ]
+        ]
+    }
+
     // ==================================================================================
     // plotting and reports
     // ==================================================================================

conf/test.config

@@ -55,4 +55,8 @@ params {
 
     // Other
     round_digits = 3
+
+    // DECOUPLER
+    decoupler_network     = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/progeny/mouse_network.tsv'
+
 }

conf/test_rnaseq_dream.config

@@ -55,4 +55,7 @@ params {
 
     // Other
     round_digits = 3
+
+    // DECOUPLER
+    decoupler_network     = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/progeny/mouse_network.tsv'
 }

conf/test_rnaseq_limma.config

@@ -61,4 +61,7 @@ params {
 
     // Other
     round_digits = 3
+
+    // DECOUPLER
+    decoupler_network     = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/progeny/mouse_network.tsv'
 }

docs/output.md

@@ -14,6 +14,8 @@ This directory contains the main reporting output of the workflow.
 - `report/`
   - `*_[Quarto notebook name].html`: an HTML report file named according to the value of `params.study_name`, containing graphical and tabular summary results for the workflow run.
   - `*.zip`: a zip file containing a Quarto notebook file with parameters set and all necessary input files to open and customise the reporting.
+  - `gsea/`: Directory containing graphical outputs from GSEA (where enabled). Plots are stored in directories named for the associated contrast.
+    - `[contrast]/png/[gsea_plot_type].png`
 
 </details>
 
@@ -38,8 +40,6 @@ Stand-alone graphical outputs are placed in this directory. They may be useful i
     - `[contrast]/png/volcano.png`: Volcano plots of -log(10) p value agains log(2) fold changes
   - `immunedeconv/`: Directory containing graphical outputs of immunedeconv results
     - `${prefix}.plot1_stacked_bar_chart.png`
-  - `gsea/`: Directory containing graphical outputs from GSEA (where enabled). Plots are stored in directories named for the associated contrast.
-    - `[contrast]/png/[gsea_plot_type].png`
   - `gprofiler2/`: Directory containing graphical outputs from gprofiler2 (where enabled). Plots are stored in directories named for the associated contrast.
     - `[contrast]/[contrast].gprofiler2.[source].gostplot.html`: An interactive gprofiler2 Manhattan plot of enriched pathways from one specific source/database, e.g. REAC
     - `[contrast]/[contrast].gprofiler2.[source].gostplot.png`: A static gprofiler2 Manhattan plot of enriched pathways from one specific source/database, e.g. REAC
@@ -49,8 +49,8 @@ Stand-alone graphical outputs are placed in this directory. They may be useful i
     - `[contrast]/[norm_function].normalized_mean_variance_relationship.png`: Plots of log intensity vs mean log intensity after normalization of each contrast level.
     - `[contrast]/[norm_function].normalized_distributions.png`: A plot of sample distributions after normalization.
     - `[contrast]/raw_distributions.png`: A plot of sample distributions without normalization.
-
-</details>
+  - `decoupler/`: Directory containing plots of decoupler results - `[differential_method]_[contrast_name]_[decoupler_method]_estimate_decoupler_plot.png`: contains the plot for the estimated activity scores for each regulator (rows) across all samples (columns).
+  </details>
 
 Most plots are included in the HTML report (see above), but are also included in static files in this folder to facilitate use in external reporting.
 
@@ -78,6 +78,9 @@ Most plots are included in the HTML report (see above), but are also included in
   - `gprofiler2/`: Directory containing tables of differential gene set analyis from gprofiler2 (where enabled)
     - `[contrast]/[contrast].gprofiler2.all_enriched_pathways.tsv`: A gprofiler2 report table for all enrichment results
     - `[contrast]/[contrast].gprofiler2.[source].sub_enriched_pathways.tsv`: A gprofiler2 report table of enriched pathways from one specific source/database, e.g. REAC
+  - `decoupler/`: Directory containing tables of decoupler results
+    - `[differential_method]_[contrast_name]_[decoupler_method]_estimate_decoupler.tsv`: contains the estimated activity scores for each regulator (rows) across all samples (columns).
+    - `[differential_method]_[contrast_name]_[decoupler_method]_pvals_decoupler.tsv`: contains the associated p-values for those activity scores, when the method supports statistical significance estimation.
   - `proteus/`: If `--study_type maxquant`: Directory containing abundance values produced by the proteus module which is used for processing MaxQuant input. Files are prefixed with the associated contrast and chosen normalization function (if any).
     - `[contrast]/[norm_function].normalized_proteingroups_tab.tsv`: Abundance table after normalization.
     - `[contrast]/raw_proteingroups_tab.tsv`: Abundance table without normalization.
@@ -92,7 +95,7 @@ The `differential` folder is likely to be the core result set for most users, co
 <summary>Output files</summary>
 
 - `shinyngs_app/`
-  - `[study name]`:
+  - `[study_name]`:
     - `data.rds`: serialized R object which can be used to generate a Shiny application
     - `app.R`: minimal R script that will source the data object and generate the app